thoughtful-turtle alpha
3D UNet Lateral Root Primordia Cells
Adrian Wolny, Lorenzo Cerrone
10.5281/zenodo.6334777/7765026
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Model Information
Description: A 3D U-Net trained to predict the cell boundaries in lightsheet stacks of Arabidopsis Lateral Root Primordia. (0.25x0.1625x0.1625) microns ZYX
Task: 3D cell segmentation
Licence: MIT
Tags: 3D, cell membrane, arabidopsis lateral root, tissue, light sheet microscopy, semantic segmentation, ilastik, U-Net, plantseg, pytorch, plant
Benchmarking
This model was not tested on datasets with reference annotations, so we cannot produce benchmarking metrics.
Model predictions
| Study | Dataset | Original image | Prediction | Analysis parameters |
|---|---|---|---|---|
| S-BIAD1490 | Source data | 
Download | 
Download | z_slices_analysed: 9,19 xy_image_crop_size: 512,512 t_slices_analysed: 0,1 |
| S-BIAD827 | Experiment A | 
Download | 
Download | z_slices_analysed: 27,37 input_channel_analysed: 0 |
| S-BIAD915 | Microscopy data | 
Download | 
Download | z_slices_analysed: 56,66 xy_image_crop_size: 1024,1024 input_channel_analysed: 1 |
| S-BIAD1241 | Colocalization N. benthamiana | 
Download | 
Download | z_slices_analysed: 12,22 input_channel_analysed: 0 |